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* gnu: python-flit: Update to 3.2.0.Ricardo Wurmus2021-04-13
| | | | | | | | | | * gnu/packages/python-xyz.scm (python-flit): Update to 3.2.0. [source]: Fetch from git repository to include flit_core. [arguments]: Add phases to bootstrap the build. [propagated-inputs]: Add python-pytoml and python-toml. [native-inputs]: Add python-docutils, python-responses, python-pygments-github-lexers, python-pytest, python-pytest-cov, python-sphinx, python-sphinxcontrib-github-alt, and python-testpath.
* gnu: Add python-sphinxcontrib-github-alt.Ricardo Wurmus2021-04-13
| | | | * gnu/packages/sphinx.scm (python-sphinxcontrib-github-alt): New variable.
* gnu: Add python-requests-unixsocket.Ricardo Wurmus2021-04-13
| | | | * gnu/packages/python-web.scm (python-requests-unixsocket): New variable.
* gnu: Add python-pygments-github-lexers.Ricardo Wurmus2021-04-13
| | | | * gnu/packages/python-xyz.scm (python-pygments-github-lexers): New variable.
* gnu: Add python-pytoml.Ricardo Wurmus2021-04-13
| | | | * gnu/packages/python-build.scm (python-pytoml): New variable.
* gnu: Remove python2-ipykernel.Ricardo Wurmus2021-04-13
| | | | | * gnu/packages/python-xyz.scm (python2-ipykernel): Remove variable. (python-ipykernel)[properties]: Remove python2-variant.
* gnu: Remove python2-jupyter-console.Ricardo Wurmus2021-04-13
| | | | | * gnu/packages/python-xyz.scm (python2-jupyter-console): Remove variable. (python-jupyter-console)[properties]: Remove python2-variant.
* gnu: Remove python2-jupyter-core.Ricardo Wurmus2021-04-13
| | | | * gnu/packages/python-xyz.scm (python2-jupyter-core): Remove variable.
* gnu: Remove python2-ipyparallel.Ricardo Wurmus2021-04-13
| | | | * gnu/packages/python-xyz.scm (python2-ipyparallel): Remove variable.
* gnu: Remove python2-matplotlib-documentation.Ricardo Wurmus2021-04-13
| | | | * gnu/packages/python-xyz.scm (python2-matplotlib-documentation): Remove variable.
* gnu: python-nbformat: Update to 5.1.3.Ricardo Wurmus2021-04-13
| | | | | | | | * gnu/packages/python-xyz.scm (python-nbformat): Update to 5.1.3. [arguments]: Remove to enable tests. [native-inputs]: Add python-pytest. [properties]: Add python2-variant. (python2-nbformat): Keep at version 4.4.0; override version and source field.
* gnu: python-nbconvert: Update to 6.0.7.Ricardo Wurmus2021-04-13
| | | | | | | | | | * gnu/packages/python-xyz.scm (python-nbconvert): Update to 6.0.7. [arguments]: Remove configure flags, enable tests, override check phase. [propagated-inputs]: Add python-defusedxml, python-nbclient, python-pandocfilters, python-jupyterlab-pygments, and python-testpath. [properties]: Add python2-variant. (python2-nbconvert): Override version, source, arguments, and propagated-inputs.
* gnu: Add python-nbclient.Ricardo Wurmus2021-04-13
| | | | * gnu/packages/jupyter.scm (python-nbclient): New variable.
* gnu: Add python-jupyterlab-pygments.Ricardo Wurmus2021-04-13
| | | | * gnu/packages/jupyter.scm (python-jupyterlab-pygments): New variable.
* gnu: Add python-nest-asyncio.Ricardo Wurmus2021-04-13
| | | | * gnu/packages/python-xyz.scm (python-nest-asyncio): New variable.
* gnu: python-notebook: Update inputs.Ricardo Wurmus2021-04-13
| | | | | | | | | | * gnu/packages/python-xyz.scm (python-notebook)[propagated-inputs]: Add python-argon2-cffi, python-ipykernel, python-ipython-genutils, python-jinja2, python-jupyter-client, python-pyzmq, python-tornado-6, and python-traitlets. [native-inputs]: Remove python-nose and python-sphinx; add python-coverage, python-nbval, python-pytest, python-pytest-cov, and python-requests-unixsocket. [arguments]: Use pytest instead of nosetests.
* gnu: python-notebook: Update to 6.3.0.Ricardo Wurmus2021-04-13
| | | | * gnu/packages/python-xyz.scm (python-notebook): Update to 6.3.0.
* gnu: python-widgetsnbextension: Add missing inputs.Ricardo Wurmus2021-04-13
| | | | | * gnu/packages/python-xyz.scm (python-widgetsnbextension)[propagated-inputs]: Add python-argon2-cffi and python-terminado.
* gnu: python-ipykernel: Update to 5.5.3.Ricardo Wurmus2021-04-13
| | | | * gnu/packages/python-xyz.scm (python-ipykernel): Update to 5.5.3.
* gnu: python-jupyter-client: Update to 6.1.12.Ricardo Wurmus2021-04-13
| | | | | | * gnu/packages/python-xyz.scm (python-jupyter-client): Update to 6.1.12. [propagated-inputs]: Add python-dateutil and python-tornado-6. [native-inputs]: Add python-pytest.
* gnu: python-jupyter-core: Update to 4.7.1.Ricardo Wurmus2021-04-13
| | | | * gnu/packages/python-xyz.scm (python-jupyter-core): Update to 4.7.1.
* gnu: python-terminado: Update to 0.9.4.Ricardo Wurmus2021-04-13
| | | | | | | | * gnu/packages/python-web.scm (python-terminado): Update to 0.9.4. [propagated-inputs]: Replace python-tornado with python-tornado-6. [native-inputs]: Replace python-nose with python-pytest. [home-page]: Follow redirect. [arguments]: Update check phase.
* gnu: esbuild: Update to 0.11.9.Ryan Prior2021-04-13
| | | | | | * gnu/packages/web.scm (esbuild): Update to 0.11.9. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
* gnu: visidata: Update to 2.4.Ryan Prior2021-04-13
| | | | | | * gnu/packages/visidata.scm (visidata): Update to 2.4. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
* gnu: gnu-standards: Update to 2020-11-25.Morgan Smith2021-04-13
| | | | | | | | * gnu/packages/gnu-doc.scm (gnu-standards): Update to 2020-11-25. [source]: Make file-name more descriptive. Use version variable for revision. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
* gnu: Add texlive-xcharter.Paul Garlick2021-04-13
| | | | * gnu/packages/tex.scm: New variable.
* gnu: guile-picture-language: Update to 0.0.1-5.a1322bf.Ricardo Wurmus2021-04-12
| | | | | * gnu/packages/guile-xyz.scm (guile-picture-language): Update to 0.0.1-5.a1322bf.
* gnu: racket: Don't inject store paths into Racket files.Philip McGrath2021-04-12
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | Apparently, during grafting, Guix can somehow mangle compiled Racket CS files (.zo) such that Racket will refuse to load them. (Maybe it has something to do with compression?) So, we stop patching Racket sources with absolute paths to store files (i.e. for foreign libraries to dlopen). Instead, we put them in a data file that doesn't get compiled or, in one case, embed it in C. Fixes https://issues.guix.gnu.org/47064 * gnu/packages/patches/racket-sh-via-rktio.patch: New file. Adds a special case at the C level, controlled by a preprocessor macro, to handle attempts to execute "/bin/sh". * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/scheme.scm (racket)[source](patches): Apply it. (racket)[arguments](#:configure-flags): Add the CPP flag to enable it. (racket)[arguments](#:modules): Use srfi-1. (racket)[arguments](#:phases): Remove 'patch-/bin/sh and 'pre-configure. Change 'pre-configure-minimal to just change directory. Add 'patch-config.rktd-lib-search-dirs after 'build and before 'install to configure Racket's "lib-search-dirs". (racket, racket-minimal)[inputs]: Add bash-minimal as an explicit input. (racket-minimal)[source]: Adjust to inherit patches from racket. (racket-minimal)[arguments]: Inherit from racket: changes no longer needed. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: Add r-txdb-dmelanogaster-ucsc-dm6-ensgene.hli2021-04-12
| | | | | | | * gnu/packages/bioconductor.scm (r-txdb-dmelanogaster-ucsc-dm6-ensgene): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
* gnu: Add cl-bodge-queue.Adam Kandur2021-04-12
| | | | | | | * gnu/packages/lisp-xyz.scm (sbcl-bodge-queue, cl-bodge-queue, ecl-bodge-queue): New variables. Co-authored-by: Guillaume Le Vaillant <glv@posteo.net>
* gnu: hydrogen: Update to 1.0.2.Nicolas Goaziou2021-04-12
| | | | * gnu/packages/music.scm (hydrogen): Update to 1.0.2.
* gnu: Add openvdb.Ekaitz Zarraga2021-04-12
| | | | | | * gnu/packages/graphics.scm (openvdb): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
* gnu: Add texlive-newtx.Paul Garlick2021-04-12
| | | | * gnu/packages/tex.scm: New variable.
* gnu: java-eclipse-jetty-util: Update to 9.4.39 [security fixes].Julien Lepiller2021-04-12
| | | | | | | | | | | | | | Fixes CVE-2021-28165 - jetty server high CPU when client send data length > 17408, CVE-2021-28164 - Normalize ambiguous URIs and CVE-2021-28163 - Exclude webapps directory from deployment scan. * gnu/packages/java.scm (java-eclipse-jetty-util): Update to 9.4.39. (java-eclipse-jetty-util-ajax): New variable. (java-eclipse-jetty-util, java-eclipse-jetty-io, java-eclipse-jetty-http) (java-eclipse-jetty-jmx, java-eclipse-jetty-server) (java-eclipse-jetty-security, java-eclipse-jetty-servlet) (java-eclipse-jetty-xml, java-eclipse-jetty-webapp): Disable tests. [native-inputs]: Remove test dependencies.
* gnu: hangups: Run test suite.Efraim Flashner2021-04-12
| | | | | * gnu/packages/messaging.scm (hangups)[arguments]: Use custom 'check phase.
* gnu: hangups: Loosen version restrictions further.Efraim Flashner2021-04-12
| | | | | * gnu/packages/messaging.scm (hangups)[arguments]: Adjust custom 'relax-dependencies phase to allow more dependency versions.
* gnu: python-mechanicalsoup: Update to 1.0.0.Ekaitz Zarraga2021-04-12
| | | | | | | | | | | * gnu/packages/python-web.scm (python-mechanicalsoup): Update to 1.0.0. [arguments]: Enable tests. [native-inputs]: Add python-pytest-flake8, python-pytest-httpbin, python-pytest-cov, python-pytest-mock, python-pytest-runner, python-requests-mock. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
* gnu: renpy: Update to 7.4.4.Leo Prikler2021-04-12
| | | | | * gnu/packages/game-development.scm (python2-renpy): Update to 7.4.4. (python2-pygame-sdl2)[renpy-version]: Likewise.
* gnu: nginx: Enable stream module.methuselah-02021-04-12
| | | | | | * gnu/packages/web.scm (nginx)[arguments]: Add --with-stream option in the 'configure phase. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: Add prips.methuselah-02021-04-12
| | | | | | gnu/packages/admin.scm (prips): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: blis: Add deprecated aliases.Ludovic Courtès2021-04-12
| | | | | | | Add deprecated aliases for packages removed in the parent commit. * gnu/packages/maths.scm (blis-sandybridge, blis-haswell, blis-knl): New variables.
* gnu: blis: Update to 0.8.1.Philip McGrath2021-04-12
| | | | | | | | | | | | | | | | | | | | | | * gnu/packages/maths.scm (make-blis): Remove internal function. Inline into ... (bliss): ... this variable. Update to 0.8.1. [native-inputs]: Add "python" and "perl". [arguments]: Adjust 'configure' phase to take advantage of new support for "configuration families" with runtime hardware detection. Select configuration automatically based on target systems, and allow "--blis-config=" in #:configure-flags to override the default. When building for x86_64, include all supported microarchetecture specializations. Add "--enable-verbose-make" configure flag for better build logs. Stop ignoring other flags from #:configure-flags. Remove explicit #:substitutable? argument: the package is now always substitutable. Add (srfi srfi-1) to #:modules. (blis/x86_64): Remove internal macro. (blis-sandybridge): Remove package: included in 'blis'. (blis-haswell): Remove package: included in 'blis'. (blis-knl): Remove package: included in 'blis'. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: monero-gui: Update to 0.17.2.0.Guillaume Le Vaillant2021-04-12
| | | | * gnu/packages/finance.scm (monero-gui): Update to 0.17.2.0.
* gnu: monero: Update to 0.17.2.0.Guillaume Le Vaillant2021-04-12
| | | | * gnu/packages/finance.scm (monero): Update to 0.17.2.0.
* gnu: newlib-nano: Fix nano lib and header paths.Morgan Smith2021-04-12
| | | | | | | * gnu/packages/embedded.scm (newlib-nano-arm-none-eabi)[arguments]: Hard link library files from *.a to *_nano.a. Hard link newlib.h to a common location. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
* gnu: electron-cash: Add missing input.Guillaume Le Vaillant2021-04-12
| | | | | | Fixes <https://bugs.gnu.org/47654>. * gnu/packages/finance.scm (electron-cash)[inputs]: Add python-pathvalidate.
* gnu: Add python-pathvalidate.Guillaume Le Vaillant2021-04-12
| | | | * gnu/packages/python-xyz.scm (python-pathvalidate): New variable.
* gnu: Add python-allpairspy.Guillaume Le Vaillant2021-04-12
| | | | * gnu/packages/python-check.scm (python-allpairspy): New variable.
* gnu: Syncthing: Update to 1.15.1 [fixes CVE-2021-21404].Leo Famulari2021-04-11
| | | | | | | | | * gnu/packages/syncthing.scm (syncthing): Update to 1.15.1. [source]: Use bundled dependencies. [inputs]: Remove field. [arguments]: Adjust the custom 'build' and 'install' phases for 1.15.1. Signed-off-by: Leo Famulari <leo@famulari.name>
* gnu: python-cython: Update to 0.29.22.Tobias Geerinckx-Rice2021-04-12
| | | | * gnu/packages/python-xyz.scm (python-cython): Update to 0.29.22.
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